BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 001995
(985 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|B Chain B, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|C Chain C, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|D Chain D, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
Length = 591
Score = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 34/110 (30%), Positives = 55/110 (50%), Gaps = 17/110 (15%)
Query: 298 FLVLDDVWTEEPQNWEQLLGCLRCGSKESRILVTTRNEKVAIAIGTTKFNIIPIEL-LSD 356
L+LDDVW +W L+ + +IL+TTR++ V ++ K+ ++P+E L
Sbjct: 239 LLILDDVW----DSW-----VLKAFDSQCQILLTTRDKSVTDSVMGPKY-VVPVESSLGK 288
Query: 357 EDCWSIFSQLALSRRLDIEESENFENIGRQIVSKCKGLPLAVKTLGSLLR 406
E I S ++ D+ E I+ +CKG PL V +G+LLR
Sbjct: 289 EKGLEILSLFVNMKKADLPEQ------AHSIIKECKGSPLVVSLIGALLR 332
>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
Length = 1263
Score = 47.4 bits (111), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 34/110 (30%), Positives = 55/110 (50%), Gaps = 17/110 (15%)
Query: 298 FLVLDDVWTEEPQNWEQLLGCLRCGSKESRILVTTRNEKVAIAIGTTKFNIIPIEL-LSD 356
L+LDDVW +W L+ + +IL+TTR++ V ++ K+ ++P+E L
Sbjct: 245 LLILDDVW----DSW-----VLKAFDSQCQILLTTRDKSVTDSVMGPKY-VVPVESSLGK 294
Query: 357 EDCWSIFSQLALSRRLDIEESENFENIGRQIVSKCKGLPLAVKTLGSLLR 406
E I S ++ D+ E I+ +CKG PL V +G+LLR
Sbjct: 295 EKGLEILSLFVNMKKADLPEQ------AHSIIKECKGSPLVVSLIGALLR 338
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/110 (30%), Positives = 55/110 (50%), Gaps = 17/110 (15%)
Query: 298 FLVLDDVWTEEPQNWEQLLGCLRCGSKESRILVTTRNEKVAIAIGTTKFNIIPIEL-LSD 356
L+LDDVW +P W L+ + +IL+TTR++ V ++ K +++P+E L
Sbjct: 239 LLILDDVW--DP--W-----VLKAFDNQCQILLTTRDKSVTDSVMGPK-HVVPVESGLGR 288
Query: 357 EDCWSIFSQLALSRRLDIEESENFENIGRQIVSKCKGLPLAVKTLGSLLR 406
E I S ++ D+ I+ +CKG PL V +G+LLR
Sbjct: 289 EKGLEILSLFVNMKKEDLPAE------AHSIIKECKGSPLVVSLIGALLR 332
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 40.0 bits (92), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 33/110 (30%), Positives = 54/110 (49%), Gaps = 17/110 (15%)
Query: 298 FLVLDDVWTEEPQNWEQLLGCLRCGSKESRILVTTRNEKVAIAIGTTKFNIIPIEL-LSD 356
L+LDDVW +P W L+ + +IL+TT ++ V ++ K +++P+E L
Sbjct: 246 LLILDDVW--DP--W-----VLKAFDNQCQILLTTSDKSVTDSVMGPK-HVVPVESGLGR 295
Query: 357 EDCWSIFSQLALSRRLDIEESENFENIGRQIVSKCKGLPLAVKTLGSLLR 406
E I S ++ D+ I+ +CKG PL V +G+LLR
Sbjct: 296 EKGLEILSLFVNMKKEDLPAE------AHSIIKECKGSPLVVSLIGALLR 339
>pdb|3RGX|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
pdb|3RGZ|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
Length = 768
Score = 36.2 bits (82), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 614 VGQIPKGIKKLIHLRYLALGENPWIKELPEALCELCN-LQTLDVSLCHYLKRLPERIG 670
VG IP L L+YL+L EN + E+P+ L C+ L LD+S H+ +P G
Sbjct: 260 VGPIPP--LPLKSLQYLSLAENKFTGEIPDFLSGACDTLTGLDLSGNHFYGAVPPFFG 315
Score = 33.5 bits (75), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 29/57 (50%)
Query: 614 VGQIPKGIKKLIHLRYLALGENPWIKELPEALCELCNLQTLDVSLCHYLKRLPERIG 670
G+IP G+ +L +++L N E+P+ + L NL L +S + +P +G
Sbjct: 479 TGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAILKLSNNSFSGNIPAELG 535
Score = 32.3 bits (72), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 31/64 (48%)
Query: 615 GQIPKGIKKLIHLRYLALGENPWIKELPEALCELCNLQTLDVSLCHYLKRLPERIGQLIN 674
G IPK I + +L L LG N +P+ + +L L LD+S R+P+ + L
Sbjct: 646 GYIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIPQAMSALTM 705
Query: 675 LRHL 678
L +
Sbjct: 706 LTEI 709
Score = 30.8 bits (68), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 33/72 (45%)
Query: 615 GQIPKGIKKLIHLRYLALGENPWIKELPEALCELCNLQTLDVSLCHYLKRLPERIGQLIN 674
G+IP+ + + L L L N E+P L NL + +S +P+ IG+L N
Sbjct: 456 GEIPQELMYVKTLETLILDFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLEN 515
Query: 675 LRHLMNSKEEWS 686
L L S +S
Sbjct: 516 LAILKLSNNSFS 527
>pdb|3RIZ|A Chain A, Crystal Structure Of The Plant Steroid Receptor Bri1
Ectodomain
pdb|3RJ0|A Chain A, Plant Steroid Receptor Bri1 Ectodomain In Complex With
Brassinolide
Length = 772
Score = 36.2 bits (82), Expect = 0.100, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 614 VGQIPKGIKKLIHLRYLALGENPWIKELPEALCELCN-LQTLDVSLCHYLKRLPERIG 670
VG IP L L+YL+L EN + E+P+ L C+ L LD+S H+ +P G
Sbjct: 257 VGPIPP--LPLKSLQYLSLAENKFTGEIPDFLSGACDTLTGLDLSGNHFYGAVPPFFG 312
Score = 33.5 bits (75), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 29/57 (50%)
Query: 614 VGQIPKGIKKLIHLRYLALGENPWIKELPEALCELCNLQTLDVSLCHYLKRLPERIG 670
G+IP G+ +L +++L N E+P+ + L NL L +S + +P +G
Sbjct: 476 TGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLENLAILKLSNNSFSGNIPAELG 532
Score = 32.3 bits (72), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 31/64 (48%)
Query: 615 GQIPKGIKKLIHLRYLALGENPWIKELPEALCELCNLQTLDVSLCHYLKRLPERIGQLIN 674
G IPK I + +L L LG N +P+ + +L L LD+S R+P+ + L
Sbjct: 643 GYIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIPQAMSALTM 702
Query: 675 LRHL 678
L +
Sbjct: 703 LTEI 706
Score = 30.8 bits (68), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 33/72 (45%)
Query: 615 GQIPKGIKKLIHLRYLALGENPWIKELPEALCELCNLQTLDVSLCHYLKRLPERIGQLIN 674
G+IP+ + + L L L N E+P L NL + +S +P+ IG+L N
Sbjct: 453 GEIPQELMYVKTLETLILDFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIGRLEN 512
Query: 675 LRHLMNSKEEWS 686
L L S +S
Sbjct: 513 LAILKLSNNSFS 524
>pdb|1OGQ|A Chain A, The Crystal Structure Of Pgip (Polygalacturonase
Inhibiting Protein), A Leucine Rich Repeat Protein
Involved In Plant Defense
Length = 313
Score = 35.8 bits (81), Expect = 0.11, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 28/62 (45%)
Query: 614 VGQIPKGIKKLIHLRYLALGENPWIKELPEALCELCNLQTLDVSLCHYLKRLPERIGQLI 673
VG IP I KL L YL + +P+ L ++ L TLD S LP I L
Sbjct: 90 VGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVTLDFSYNALSGTLPPSISSLP 149
Query: 674 NL 675
NL
Sbjct: 150 NL 151
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 32.7 bits (73), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 47/85 (55%), Gaps = 9/85 (10%)
Query: 564 SEMVPFPSMVYDE-TKLRSLVL-DQRLSFKPRIALSKLFDRLTCLRSIDGL--PVGQIPK 619
+++ P V+D T+L L L +L+ P S +FDRL L+ + + ++P+
Sbjct: 74 NQLGALPVGVFDSLTQLTVLDLGTNQLTVLP----SAVFDRLVHLKELFMCCNKLTELPR 129
Query: 620 GIKKLIHLRYLALGENPWIKELPEA 644
GI++L HL +LAL +N +K +P
Sbjct: 130 GIERLTHLTHLALDQN-QLKSIPHG 153
Score = 32.3 bits (72), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 47/90 (52%), Gaps = 7/90 (7%)
Query: 618 PKGIKKLIHLRYLALGENPWIKELPEALCE-LCNLQTLDVSLCHYLKRLPERI-GQLINL 675
P LI+L+ L LG N + LP + + L L LD+ + L LP + +L++L
Sbjct: 57 PGVFDSLINLKELYLGSN-QLGALPVGVFDSLTQLTVLDLGT-NQLTVLPSAVFDRLVHL 114
Query: 676 RHLMNSKEEWSRLSYMPRGMERLTGLRTLG 705
+ L ++L+ +PRG+ERLT L L
Sbjct: 115 KELFMC---CNKLTELPRGIERLTHLTHLA 141
>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 727
Score = 31.6 bits (70), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 46/104 (44%), Gaps = 5/104 (4%)
Query: 578 KLRSLVLDQRLSFKPRIAL---SKLFDRLTCLRSIDGLPVGQIPKGIKKLIHLRYLALGE 634
KL +D+ + R+ + SK D+L + L + I I K L L L
Sbjct: 197 KLSQYSIDEDDDIENRMVMPKDSKYDDQLWHALDLSNLQIFNISANIFKYDFLTRLYLNG 256
Query: 635 NPWIKELPEALCELCNLQTLDVSLCHYLKRLPERIGQLINLRHL 678
N + ELP + L NL+ LD+S + L LP +G L++
Sbjct: 257 NS-LTELPAEIKNLSNLRVLDLS-HNRLTSLPAELGSCFQLKYF 298
>pdb|3RFS|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
pdb|3RFS|B Chain B, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 272
Score = 30.8 bits (68), Expect = 3.9, Method: Composition-based stats.
Identities = 31/88 (35%), Positives = 53/88 (60%), Gaps = 8/88 (9%)
Query: 619 KGIKKLIHLRYLALGENPWIKELPEALCELCNLQTLDVSLCHYLKRLPERI-GQLINLRH 677
+GI+ L ++RYLALG N + ++ AL EL NL L ++ + L+ LP + +L NL+
Sbjct: 57 QGIQYLPNVRYLALGGNK-LHDI-SALKELTNLTYLILT-GNQLQSLPNGVFDKLTNLKE 113
Query: 678 LMNSKEEWSRLSYMPRGM-ERLTGLRTL 704
L+ + ++L +P G+ ++LT L L
Sbjct: 114 LVLVE---NQLQSLPDGVFDKLTNLTYL 138
>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 279
Score = 30.8 bits (68), Expect = 4.0, Method: Composition-based stats.
Identities = 31/88 (35%), Positives = 53/88 (60%), Gaps = 8/88 (9%)
Query: 619 KGIKKLIHLRYLALGENPWIKELPEALCELCNLQTLDVSLCHYLKRLPERI-GQLINLRH 677
+GI+ L ++RYLALG N + ++ AL EL NL L ++ + L+ LP + +L NL+
Sbjct: 57 QGIQYLPNVRYLALGGNK-LHDI-SALKELTNLTYLILT-GNQLQSLPNGVFDKLTNLKE 113
Query: 678 LMNSKEEWSRLSYMPRGM-ERLTGLRTL 704
L+ + ++L +P G+ ++LT L L
Sbjct: 114 LVLVE---NQLQSLPDGVFDKLTNLTYL 138
>pdb|3QFL|A Chain A, Coiled-Coil Domain-Dependent Homodimerization Of
Intracellular Mla Immune Receptors Defines A Minimal
Functional Module For Triggering Cell Death
Length = 115
Score = 29.3 bits (64), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 47/82 (57%), Gaps = 6/82 (7%)
Query: 4 AIVSTILEQLALILVEQTAAGVRLIAGAEEEVENLHRRFHLIKA-VVEDAE-KRQMKETA 61
A +S ++ +L +L E+ +L G ++ +E+L + A +++ E R+ ++
Sbjct: 1 AAISNLIPKLGELLTEE----FKLHKGVKKNIEDLGKELESXNAALIKIGEVPREQLDSQ 56
Query: 62 VRVWLDDLKHASYDMEDVLDEW 83
++W D+++ SY +EDV+D++
Sbjct: 57 DKLWADEVRELSYVIEDVVDKF 78
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.136 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,510,559
Number of Sequences: 62578
Number of extensions: 1020203
Number of successful extensions: 2267
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 2244
Number of HSP's gapped (non-prelim): 33
length of query: 985
length of database: 14,973,337
effective HSP length: 108
effective length of query: 877
effective length of database: 8,214,913
effective search space: 7204478701
effective search space used: 7204478701
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)